def seperate_parents_and_children(feature_db):
parent_dict, child_dict, intermediate_dict = {}, {}, {}
feature_types = feature_db.featuretypes()
parent_types, child_types, intermediate_types = find_feature_type_order(
feature_types, feature_db)
feature_num = 0
for parent_type in parent_types:
for parent in feature_db.features_of_type(featuretype=parent_type):
feature_num += 1
parent_dict[parent.id] = parent
child_dict[parent.id] = []
for child_type in child_types:
for child in feature_db.children(parent,
featuretype=child_type):
child_dict[parent.id].append(child)
if "Parent" not in child.attributes:
add_parent_tag(child, feature_db)
if len(child_dict[parent.id]) == 0:
child_dict[parent.id].append(parent)
for intermediate_type in intermediate_types:
for intermediate_feature in feature_db.features_of_type(
featuretype=intermediate_type):
intermediate_dict[intermediate_feature.id] = intermediate_feature
if "Parent" not in intermediate_feature.attributes:
add_parent_tag(intermediate_feature, feature_db)
parent_order = liftoff_utils.find_parent_order([
parent for parent in list(parent_dict.values()) if parent is not None
])
return parent_dict, child_dict, intermediate_dict, parent_order
def check_homologues(all_lifted_features, lifted_features_to_check, parent_dict, original_parent_order):
all_feature_list = liftoff_utils.get_parent_list(all_lifted_features, parent_dict)
features_to_check_list = liftoff_utils.get_parent_list(lifted_features_to_check, parent_dict)
all_feature_list.sort(key = lambda x: (x.seqid, x.start))
new_parent_order = liftoff_utils.find_parent_order(all_feature_list)
chrom_index_dict = {}
feature_index = 0
for feature in all_feature_list:
if feature.seqid not in chrom_index_dict:
chrom_index_dict[feature.seqid] = feature_index
feature_index += 1
remap_features = {}
for feature in features_to_check_list:
nearby_features = all_feature_list[chrom_index_dict[feature.seqid]:]
compare_nearby_features(nearby_features, parent_dict, feature, remap_features, original_parent_order,
new_parent_order)
return remap_features